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EMBO J. 2017 Feb 1;36(3):374-387. doi: 10.15252/embj.201694639. Epub 2016 Nov 11.

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.

Author information

1
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
2
The Roslin Institute, University of Edinburgh, Edinburgh, UK.
3
MRC Human Genetic Unit, University of Edinburgh, Edinburgh, UK.
4
Systems Biology Initiative, University of New South Wales, Sydney, NSW, Australia.
5
Peter Doherty Institute, University of Melbourne, Melbourne, Victoria, Australia.
6
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK j.tree@unsw.edu.au d.tollervey@ed.ac.uk.
7
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia j.tree@unsw.edu.au d.tollervey@ed.ac.uk.

Abstract

RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA-RNA interactions in bacteria. Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base-paired sRNA-mRNA duplexes in association with RNase E, allowing proximity-dependent ligation and sequencing of cognate sRNA-mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA-mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co-regulated target mRNAs. We identified multiple mRNA targets for the pathotype-specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli Numerous sRNA interactions were also identified with non-coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.

KEYWORDS:

CRAC ; EHEC ; CLIP‐Seq; enterohaemorrhagic E. coli; non‐coding RNA

PMID:
27836995
PMCID:
PMC5286369
DOI:
10.15252/embj.201694639
[Indexed for MEDLINE]
Free PMC Article

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